http://en.wikipedia.org/wiki/Conspiracy_(Star_Trek:_The_Next_Generation)
I guess that's the answer.
According to Captains' Logs: The Unauthorized Complete Trek Voyages, the parasites were originally intended to be working for the Borg. The destruction of the colonies in the following episode ("The Neutral Zone") would then have led into the Borg's introduction in the second season premiere. However, due to the writers' strike of 1988, the Borg storyline was pushed back several months, and divorced from any relationship to the "Conspiracy" storyline. There was no further on-screen connection or reference to the conspiracy until its mention in passing in The Drumhead in the fourth season.
Bonus Link:
http://www.tvsquad.com/bloggers/wil-wheaton/ Excruciatingly funny recaps by Will Wheaton of some of ST:TNG's episodes.